Initially he was King of Sicily, from age four. His kingdom was held for him by Pope Innocent III until he was of age.

Otto of Brunswick had been elected Holy Roman Emperor in 1209; Frederick had been elected emperor by a rebellious faction who had the backing of Innocent III in 1211 at the Diet of Nuremberg, but until the debacle at the Battle of Bouvines in 1214 this was an empty honor. After Bouvines Otto was deposed (to die in 1218), Innocent III managed to get most of the princes to renounce the excommunicated Otto and elect Frederick.

Said to be literate in 9 languages, Frederick was a very modern ruler for his times, being a patron of science and learning, and having fairly advanced views on economics. He abolished state monopolies, internal tolls, and import regulations within his empire.

He was known in his own time as the Stupor mundi, the "Wonder of the world". Frederick wrote a manual on the art of falconry, De arte venandi cum avibus ("On the art of hunting with birds"), of which many illustrated copies survive from the 13th and 14th centuries.

Frederick was banned by Pope Gregory IX in 1227 for failing to honor his promise to launch a crusade. After being banned he embarked the crusade the following year (1228), which was seen on by the pope as a rude provocation, since the church could not take any part in the honor for the crusade.

This event was the start of a long and bitter fight between Frederick and the pope (and his successor, Pope Innocent IV). This fight was mainly taken into propaganda and also related to the lombardian provinces. The opposing forces were known as the Guelfs[?] (The Lombard League[?]) and the Ghibellins[?]